During and post-ride neck pain?

I've been cycling at my local track for 2-3 months now. Over the past two weeks, there has been a pain in my neck from looking forwards/up for periods of time, about 1 hour 30min into a 2 hour session.
The neck pain doesn't stay long post-ride, but during the ride it is almost unbearable. When I purchased my bike, the LBS gave me a fit and I trust them, I've been going there for years (MTB stuff for 8 years).
The bike doesn't feel too long, or low. I only use 'modern' shallow drops, so I doubt it's the fact that the drops are too low. I can ride in the hoods all day without neck pain, but with sprinting exercises on the track, I find the pain comes then, seated sprinting in the drops. Will I adapt to the position? The bars are *exactly* the same height below the saddle (Saddle to hoods) as my old bike which I didn't get this pain on, and that had larger drops.
I'm 14 (if this has anything to with it), and the newer bike is the same size top tube as my old bike (Both Specialized) and may have a *slightly* longer stem. Surely a few mm shouldn't make this much difference?
Will my body adapt and develop the leg muscles? Or should I buy a shorter stem?

I did a search, and was surprised I didn't find anything. Sorry if this is considered the wrong area, but I thought this is where the people would be who knew about the body and cyclings effects on it.

Could you have injured the muscles there somehow? Something different about sleeping position? Have you been doing something new?

I also doubt it's entirely your fit. However a longer reach will change how your shoulder muscles work during a sprint. Are your shoulders relaxed and dropped? Is your back straight? What does your coach say?

I assume, being 14, that you don't have much time on a racing bike yet? Meaning years. Neck strength takes time to develop. Neck pain is one of the commonest complaints of riders who are ramping up their time on the bike. You could do stretching and strengthening exercises. I used to let my neck go completely slack, and then while standing or sitting, let my head flop around 360°, a number of revolutions. It's hard to get the muscles to completely let go. Football players do neck exercises where they put a strap across the back of the head and then use it to raise a weight. I'm not sure that does any good for your problem, though.

You could certainly try a shorter stem. That's a cheap thing to try. Very little down side. If you have pain every time, then you're irritating your neck every time, which won't lend itself to healing. Best try to get it fixed.

On my post I said leg muscles, I meant neck.
I really doubt it's a sleep position, and I've not been doing anything new physically. I have ridden MTB for as long as I can remember, and have entered a few races and found myself stronger than the opposition and ride MTB every Sunday for 3-4 hours, but road/track position seems lower, but comfortable.
I wouldn't call my bike a long reach, at my club there are others with significantly larger reach (proportionate to height/limb length). I would say my shoulder are relaxed, but not 'dropped'. The 'coach' doesn't really give one-on-one, he just leads the exercises.
I'll try neck stretches and give this stem another session (tonight). As it's the number one complaint, would it be because I've gone from 3-4 hours MTB on a sunday, to 2 hours Friday track and another 2 Wednesday track?

if the group your coach is working with are juniors your age, then he should really be paying attention to technique as much as doing drills.
that aside
mtb bars put you into a different position than 'drop bars.
it's hard to say much without seeing how you ride, but there are a few general things to watch/do
when in the drops, especially when either in-saddle or off for sprint or bridging, the tendency is for the elbows to pop out - work/think about pulling the shoulder blades down and in (this will also 'drop' the shoulders). this will engage the lats and traps more and provide a bit more sprinting power.
It will also disengage some of the neck muscles. Conversely, 'shrugging' while you work for more pedal power overworks the neck muscles and disengages the larger upper back muscles (traps and lats...) the opposite of what you want.
rolling the shoulder blades down and 'in' also keeps the elbows from popping out excessively, which gives you more bicep, and consequently, more forearm engagement.
When you drop those shoulders, you'll also notice a greater range of movement for the neck/head, again reducing stress up there.
at your age I don't recommend using 'weights', for a few more years I would suggest using resistance exercises, as with elastic bands. They'll build strength without as much chance of causing joint and connective tissue problems, as you continue growing/developing.

Golden rose, the color of the dream I had
Not too long ago
A misty blue and the lillac too
A never to grow old

you've most likely strained your muscles that hold your head up when cycling on the track (they have a name). it takes time to build these up. like months or years. i'd say back off for a little while and let them heal.

The coach who leads the sessions on Wednesdays (when I get the pain) does more sprinting activities than Fridays. The coach isn't working with juniors my age, just me. It's an adult session that I got invited to. Although, with the little sprinting I did yesterday I followed the advice concerning shoulders and position. I never edged my elbows out when I was sprinting, but I didn't relax my shoulder as much as I should. I tried it and I didn't get any pains, the test will come Wednesday though.
Thanks for the advice!
Side note; about the weights, I do lift, but only on the rare occasion I have nothing else to do in my lunch break.